Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions
We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P2(1) and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P2(1) was shown to yield equivalent results to P1 in simulations of bulk water,...
Gespeichert in:
| Veröffentlicht in: | Biophysical journal 2002-05, Vol.82 (5), p.2317-2325 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 2325 |
|---|---|
| container_issue | 5 |
| container_start_page | 2317 |
| container_title | Biophysical journal |
| container_volume | 82 |
| creator | Dolan, Elizabeth A Venable, Richard M Pastor, Richard W Brooks, Bernard R |
| description | We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P2(1) and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P2(1) was shown to yield equivalent results to P1 in simulations of bulk water, a water/vacuum interface, and pure DPPC bilayers with an equal number of lipids per leaflet; equivalence of Pc and P1 was also demonstrated for the former two systems. P2(1) was further tested in simulations involving the spreading of an octane film on water, and equilibration of a DPPC bilayer from an initial condition containing different numbers of lipids in the two leaflets. Lastly, a simulation in P2(1) of a DOPC/melittin membrane showed significant passage of lipids to the melittin-containing leaflet from the initial distribution, and lends insight into the condensation of lipids by melittin. |
| doi_str_mv | 10.1016/S0006-3495(02)75577-X |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1302024</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>71614999</sourcerecordid><originalsourceid>FETCH-LOGICAL-p221t-ec1cbdc2aaaddcc9e088986cc34125ec0b43fb6a2c01b75e4c2eaf61e41b7dae3</originalsourceid><addsrcrecordid>eNpdkE1LxDAQhoMo7rr6E5TgQfRQzaRpu70IsvgFCwoqeCtpMnWztMmatIL_3qCrqKdhmIeXZ15C9oGdAoP87IExliepKLNjxk-KLCuK5HmDjCETPGFsmm-S8Q8yIjshLBkDnjHYJiOAMhec8zFpHkw3tLI3zgbqGtphV3tpMVBpNXX9Aj01tkffSGVkS8N76LELdAjGvtB7fgwnn-S9oiv0xmmjaO0Gq6V_p8pZbT6jd8lWI9uAe-s5IU9Xl4-zm2R-d307u5gnK86hT1CBqrXiUkqtlSqRTaflNFcqFVEdFatF2tS55IpBXWQoFEfZ5IAirlpiOiHnX7mroe5QK7S9l2218qaLQpWTpvp7sWZRvbi3ClLGGRcx4Ggd4N3rgKGvOhMUtm3sxA2hKiAHUZZlBA__gUs3eBufqzhkRRQHHqGD3zo_Ht_9px_JSouJ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>215708812</pqid></control><display><type>article</type><title>Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions</title><source>MEDLINE</source><source>Cell Press Free Archives</source><source>Elsevier ScienceDirect Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><creator>Dolan, Elizabeth A ; Venable, Richard M ; Pastor, Richard W ; Brooks, Bernard R</creator><creatorcontrib>Dolan, Elizabeth A ; Venable, Richard M ; Pastor, Richard W ; Brooks, Bernard R</creatorcontrib><description>We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P2(1) and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P2(1) was shown to yield equivalent results to P1 in simulations of bulk water, a water/vacuum interface, and pure DPPC bilayers with an equal number of lipids per leaflet; equivalence of Pc and P1 was also demonstrated for the former two systems. P2(1) was further tested in simulations involving the spreading of an octane film on water, and equilibration of a DPPC bilayer from an initial condition containing different numbers of lipids in the two leaflets. Lastly, a simulation in P2(1) of a DOPC/melittin membrane showed significant passage of lipids to the melittin-containing leaflet from the initial distribution, and lends insight into the condensation of lipids by melittin.</description><identifier>ISSN: 0006-3495</identifier><identifier>EISSN: 1542-0086</identifier><identifier>DOI: 10.1016/S0006-3495(02)75577-X</identifier><identifier>PMID: 11964222</identifier><language>eng</language><publisher>United States: Biophysical Society</publisher><subject>1,2-Dipalmitoylphosphatidylcholine - chemistry ; Binding Sites ; Computer Simulation ; Lipid Bilayers - chemistry ; Lipids ; Membranes ; Membranes, Artificial ; Models, Molecular ; Molecular Conformation ; Octanes - chemistry ; Phosphatidylcholines - chemistry ; Software ; Structure-Activity Relationship ; Water ; Water - chemistry</subject><ispartof>Biophysical journal, 2002-05, Vol.82 (5), p.2317-2325</ispartof><rights>Copyright Biophysical Society May 2002</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302024/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302024/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11964222$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dolan, Elizabeth A</creatorcontrib><creatorcontrib>Venable, Richard M</creatorcontrib><creatorcontrib>Pastor, Richard W</creatorcontrib><creatorcontrib>Brooks, Bernard R</creatorcontrib><title>Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions</title><title>Biophysical journal</title><addtitle>Biophys J</addtitle><description>We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P2(1) and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P2(1) was shown to yield equivalent results to P1 in simulations of bulk water, a water/vacuum interface, and pure DPPC bilayers with an equal number of lipids per leaflet; equivalence of Pc and P1 was also demonstrated for the former two systems. P2(1) was further tested in simulations involving the spreading of an octane film on water, and equilibration of a DPPC bilayer from an initial condition containing different numbers of lipids in the two leaflets. Lastly, a simulation in P2(1) of a DOPC/melittin membrane showed significant passage of lipids to the melittin-containing leaflet from the initial distribution, and lends insight into the condensation of lipids by melittin.</description><subject>1,2-Dipalmitoylphosphatidylcholine - chemistry</subject><subject>Binding Sites</subject><subject>Computer Simulation</subject><subject>Lipid Bilayers - chemistry</subject><subject>Lipids</subject><subject>Membranes</subject><subject>Membranes, Artificial</subject><subject>Models, Molecular</subject><subject>Molecular Conformation</subject><subject>Octanes - chemistry</subject><subject>Phosphatidylcholines - chemistry</subject><subject>Software</subject><subject>Structure-Activity Relationship</subject><subject>Water</subject><subject>Water - chemistry</subject><issn>0006-3495</issn><issn>1542-0086</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNpdkE1LxDAQhoMo7rr6E5TgQfRQzaRpu70IsvgFCwoqeCtpMnWztMmatIL_3qCrqKdhmIeXZ15C9oGdAoP87IExliepKLNjxk-KLCuK5HmDjCETPGFsmm-S8Q8yIjshLBkDnjHYJiOAMhec8zFpHkw3tLI3zgbqGtphV3tpMVBpNXX9Aj01tkffSGVkS8N76LELdAjGvtB7fgwnn-S9oiv0xmmjaO0Gq6V_p8pZbT6jd8lWI9uAe-s5IU9Xl4-zm2R-d307u5gnK86hT1CBqrXiUkqtlSqRTaflNFcqFVEdFatF2tS55IpBXWQoFEfZ5IAirlpiOiHnX7mroe5QK7S9l2218qaLQpWTpvp7sWZRvbi3ClLGGRcx4Ggd4N3rgKGvOhMUtm3sxA2hKiAHUZZlBA__gUs3eBufqzhkRRQHHqGD3zo_Ht_9px_JSouJ</recordid><startdate>200205</startdate><enddate>200205</enddate><creator>Dolan, Elizabeth A</creator><creator>Venable, Richard M</creator><creator>Pastor, Richard W</creator><creator>Brooks, Bernard R</creator><general>Biophysical Society</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>3V.</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AF</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>S0X</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>200205</creationdate><title>Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions</title><author>Dolan, Elizabeth A ; Venable, Richard M ; Pastor, Richard W ; Brooks, Bernard R</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p221t-ec1cbdc2aaaddcc9e088986cc34125ec0b43fb6a2c01b75e4c2eaf61e41b7dae3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>1,2-Dipalmitoylphosphatidylcholine - chemistry</topic><topic>Binding Sites</topic><topic>Computer Simulation</topic><topic>Lipid Bilayers - chemistry</topic><topic>Lipids</topic><topic>Membranes</topic><topic>Membranes, Artificial</topic><topic>Models, Molecular</topic><topic>Molecular Conformation</topic><topic>Octanes - chemistry</topic><topic>Phosphatidylcholines - chemistry</topic><topic>Software</topic><topic>Structure-Activity Relationship</topic><topic>Water</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dolan, Elizabeth A</creatorcontrib><creatorcontrib>Venable, Richard M</creatorcontrib><creatorcontrib>Pastor, Richard W</creatorcontrib><creatorcontrib>Brooks, Bernard R</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>SIRS Editorial</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biophysical journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dolan, Elizabeth A</au><au>Venable, Richard M</au><au>Pastor, Richard W</au><au>Brooks, Bernard R</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions</atitle><jtitle>Biophysical journal</jtitle><addtitle>Biophys J</addtitle><date>2002-05</date><risdate>2002</risdate><volume>82</volume><issue>5</issue><spage>2317</spage><epage>2325</epage><pages>2317-2325</pages><issn>0006-3495</issn><eissn>1542-0086</eissn><abstract>We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P2(1) and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P2(1) was shown to yield equivalent results to P1 in simulations of bulk water, a water/vacuum interface, and pure DPPC bilayers with an equal number of lipids per leaflet; equivalence of Pc and P1 was also demonstrated for the former two systems. P2(1) was further tested in simulations involving the spreading of an octane film on water, and equilibration of a DPPC bilayer from an initial condition containing different numbers of lipids in the two leaflets. Lastly, a simulation in P2(1) of a DOPC/melittin membrane showed significant passage of lipids to the melittin-containing leaflet from the initial distribution, and lends insight into the condensation of lipids by melittin.</abstract><cop>United States</cop><pub>Biophysical Society</pub><pmid>11964222</pmid><doi>10.1016/S0006-3495(02)75577-X</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0006-3495 |
| ispartof | Biophysical journal, 2002-05, Vol.82 (5), p.2317-2325 |
| issn | 0006-3495 1542-0086 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1302024 |
| source | MEDLINE; Cell Press Free Archives; Elsevier ScienceDirect Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | 1,2-Dipalmitoylphosphatidylcholine - chemistry Binding Sites Computer Simulation Lipid Bilayers - chemistry Lipids Membranes Membranes, Artificial Models, Molecular Molecular Conformation Octanes - chemistry Phosphatidylcholines - chemistry Software Structure-Activity Relationship Water Water - chemistry |
| title | Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-14T03%3A20%3A17IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Simulations%20of%20membranes%20and%20other%20interfacial%20systems%20using%20P2(1)%20and%20Pc%20periodic%20boundary%20conditions&rft.jtitle=Biophysical%20journal&rft.au=Dolan,%20Elizabeth%20A&rft.date=2002-05&rft.volume=82&rft.issue=5&rft.spage=2317&rft.epage=2325&rft.pages=2317-2325&rft.issn=0006-3495&rft.eissn=1542-0086&rft_id=info:doi/10.1016/S0006-3495(02)75577-X&rft_dat=%3Cproquest_pubme%3E71614999%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=215708812&rft_id=info:pmid/11964222&rfr_iscdi=true |